Apologies for running a one-man thread, but I realised that I've now answered my
own question regarding errors with CGI, Bio::Factory::EMBOSS and taint.
Given that the EMBOSS binaries are in /usr/local/bin, adding:
$ENV{'PATH'} = '/usr/local/bin'
near the top of the script does the trick.
Neil
--
School of Molecular and Microbial Sciences
University of Queensland
Brisbane 4072 Australia
http://nsaunders.wordpress.com